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Opened 6 years ago
Closed 5 years ago
#2932 closed defect (fixed)
View transition "jumpy"
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.92 (2020-03-06) Description Camera trajectory is discontinuous for large view re-orientations. The following sequence below reproduces the problem. This seriously compromises my ability to make movies in ChimeraX. I have confirmed that Chimera (not ChimeraX) handles the equivalent transition just fine. zoom 0.5 move x -40 1 view name v1 roll y 180 1 move x 80 1 view name v2 view v1 100 view v2 100 Log: UCSF ChimeraX version: 0.92 (2020-03-06) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Error opening /Users/charlessindelar/chimerax_start/chimerax_start.py: invalid syntax (chimerax_start.py, line 1) > open > /Users/charlessindelar/Workworkwork/Talks/20_nih_job_talk/chimx_movies/AlFx_011x_7A_cc.mrc > format mrc Opened AlFx_011x_7A_cc.mrc, grid size 82,87,149, pixel 1.37,1.37,1.37, shown at level 5.65e-07, step 1, values float32 > volume #1 level 0.003079 > ui mousemode rightMode zoom > volume #1 level -0.001581 > volume #1 level 0.0005992 > volume #1 level 0.004191 > roll y 180 1 > view name v2 > roll y 180 1 > view name v1 > view v2 20 > view v2 100 > view v1 100 > view v2 100 > close session > open 1mkj format mmCIF fromDatabase pdb 1mkj title: Human Kinesin Motor Domain With Docked Neck Linker [more info...] Chain information for 1mkj #1 --- Chain | Description A | kinesin heavy chain Non-standard residues in 1mkj #1 --- ADP — adenosine-5'-diphosphate MG — magnesium ion SO4 — sulfate ion Unknown command: scale 0.5 > zoom 0.5 > move x -20 > move x -20 > close session > open 1mkj 1mkj title: Human Kinesin Motor Domain With Docked Neck Linker [more info...] Chain information for 1mkj #1 --- Chain | Description A | kinesin heavy chain Non-standard residues in 1mkj #1 --- ADP — adenosine-5'-diphosphate MG — magnesium ion SO4 — sulfate ion > open 1mkj 1mkj title: Human Kinesin Motor Domain With Docked Neck Linker [more info...] Chain information for 1mkj #2 --- Chain | Description A | kinesin heavy chain Non-standard residues in 1mkj #2 --- ADP — adenosine-5'-diphosphate MG — magnesium ion SO4 — sulfate ion > zoom 0.5 > move x -40 1 > view name v1 > roll y 180 1 > move x 80 1 > view name v2 > view v1 100 > view v2 100 > view > view > view > view > close session > open 1mkj 1mkj title: Human Kinesin Motor Domain With Docked Neck Linker [more info...] Chain information for 1mkj #1 --- Chain | Description A | kinesin heavy chain Non-standard residues in 1mkj #1 --- ADP — adenosine-5'-diphosphate MG — magnesium ion SO4 — sulfate ion > roll x 23 1 > roll y 46 1 > roll z 66 1 > zoom 0.5 > move x -40 1 > view name v1 > roll y 180 1 > move x 80 1 > view name v2 > view v1 100 > view v2 100 OpenGL version: 4.1 INTEL-10.36.19 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc.
Change History (6)
comment:1 by , 6 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → View transition "jumpy" |
follow-up: 2 comment:2 by , 6 years ago
comment:3 by , 6 years ago
I was not able to reproduce this problem with the exact same version of ChimeraX (0.92). The two last view commands produce a smooth and correct looking rotation by 180 degrees and translation. I opened 1mkj and followed exactly the commands you listed.
I suspect your problem is related to the morph problem, some numerical precision issue when handling 180 degree rotation. But I need a test case that exhibits the problem.
follow-up: 4 comment:4 by , 6 years ago
Hmmmm... this is peculiar! I just retested on my same version of Chimera, and it seems to be a sporadic problem- sometimes I can reproduce it and sometimes not. It seems to be essential, when the bug is active, to rotate the PDB model an arbitrary amount, around more than 1 axis, to make it happen at all.
However, today it stopped happening, for whatever reason on ChimeraX v 0.92 and even with stopping/restarting I am unable to reproduce it anymore at this moment.
All I can say is when it rears its ugly head, it is a pernicious problem.
Exploring a bit further, I did find I can still reproduce it consistently on older daily builds- for example, version 0.91 (daily build) downloaded 11/28/2019 or so.
In that case- here is a minimal sequence to make it happen. It seems an x-rotation is required after opening the initial model.
open 1mkj; roll x 23 1; move x -40 1; wait 1; view name v1; roll y 180 1; move x 80 1; wait 1; view name v2; view v1 100;
Interestingly, and quite perniciously, after the problem arises, it starts to intrude on "flying" that does not involve 180° transitions. For example, after doing the above, I get a strong "jumping" phenomenon with:
view orient; wait 1; view v2 100
But not with
view orient; wait 1; view v1 100
Weird!
- Chuck
On 3/10/20, 12:57 AM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
#2932: View transition "jumpy"
-----------------------------------------+-------------------------
Reporter: charles.sindelar@… | Owner: Tom Goddard
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Graphics | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-----------------------------------------+-------------------------
Comment (by Tom Goddard):
I was not able to reproduce this problem with the exact same version of
ChimeraX (0.92). The two last view commands produce a smooth and correct
looking rotation by 180 degrees and translation. I opened 1mkj and
followed exactly the commands you listed.
I suspect your problem is related to the morph problem, some numerical
precision issue when handling 180 degree rotation. But I need a test case
that exhibits the problem.
--
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follow-up: 5 comment:5 by , 6 years ago
There was a problem with computing rotation axis and angle for 180 degree rotations that I fixed a month or two ago. So only test results on current ChimeraX builds matter. If you observe it in a recent ChimeraX (from the last few weeks or newer) then give me an update.
comment:6 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
I tried this again in current ChimeraX daily build and it is perfectly smooth. I think it was caused by the 180 degree rotation bug fixed long ago.
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Hi guys! Sorry for the "core dump" of several frustrations at the same time. By the way, I should have said I continue to appreciate the massive efforts that continue to go into perfecting ChimeraX. Regarding this bug report- I figured out a bit more. It turns out the problem is specifically related to the 180° rotation about the y axis, and must be some kind of numeric issue with a matrix inversion. When I modify the y rotation to 180.00001, the problem goes away. It's sort of a "small" problem, but I have now encountered it two or more times in the past several months. Thanks again, Chuck On 3/6/20, 11:43 AM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: #2932: ChimeraX bug report submission --------------------------------+----------------------------- Reporter: charles.sindelar@… | Type: defect Status: new | Priority: normal Component: Unassigned | Blocked By: Blocking: | Notify when closed: --------------------------------+----------------------------- {{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.92 (2020-03-06) Description Camera trajectory is discontinuous for large view re-orientations. The following sequence below reproduces the problem. This seriously compromises my ability to make movies in ChimeraX. I have confirmed that Chimera (not ChimeraX) handles the equivalent transition just fine. zoom 0.5 move x -40 1 view name v1 roll y 180 1 move x 80 1 view name v2 view v1 100 view v2 100 Log: UCSF ChimeraX version: 0.92 (2020-03-06) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Error opening /Users/charlessindelar/chimerax_start/chimerax_start.py: invalid syntax (chimerax_start.py, line 1) > open > /Users/charlessindelar/Workworkwork/Talks/20_nih_job_talk/chimx_movies/AlFx_011x_7A_cc.mrc > format mrc Opened AlFx_011x_7A_cc.mrc, grid size 82,87,149, pixel 1.37,1.37,1.37, shown at level 5.65e-07, step 1, values float32 > volume #1 level 0.003079 > ui mousemode rightMode zoom > volume #1 level -0.001581 > volume #1 level 0.0005992 > volume #1 level 0.004191 > roll y 180 1 > view name v2 > roll y 180 1 > view name v1 > view v2 20 > view v2 100 > view v1 100 > view v2 100 > close session > open 1mkj format mmCIF fromDatabase pdb 1mkj title: Human Kinesin Motor Domain With Docked Neck Linker [more info...] Chain information for 1mkj #1 --- Chain | Description A | kinesin heavy chain Non-standard residues in 1mkj #1 --- ADP — adenosine-5'-diphosphate MG — magnesium ion SO4 — sulfate ion Unknown command: scale 0.5 > zoom 0.5 > move x -20 > move x -20 > close session > open 1mkj 1mkj title: Human Kinesin Motor Domain With Docked Neck Linker [more info...] Chain information for 1mkj #1 --- Chain | Description A | kinesin heavy chain Non-standard residues in 1mkj #1 --- ADP — adenosine-5'-diphosphate MG — magnesium ion SO4 — sulfate ion > open 1mkj 1mkj title: Human Kinesin Motor Domain With Docked Neck Linker [more info...] Chain information for 1mkj #2 --- Chain | Description A | kinesin heavy chain Non-standard residues in 1mkj #2 --- ADP — adenosine-5'-diphosphate MG — magnesium ion SO4 — sulfate ion > zoom 0.5 > move x -40 1 > view name v1 > roll y 180 1 > move x 80 1 > view name v2 > view v1 100 > view v2 100 > view > view > view > view > close session > open 1mkj 1mkj title: Human Kinesin Motor Domain With Docked Neck Linker [more info...] Chain information for 1mkj #1 --- Chain | Description A | kinesin heavy chain Non-standard residues in 1mkj #1 --- ADP — adenosine-5'-diphosphate MG — magnesium ion SO4 — sulfate ion > roll x 23 1 > roll y 46 1 > roll z 66 1 > zoom 0.5 > move x -40 1 > view name v1 > roll y 180 1 > move x 80 1 > view name v2 > view v1 100 > view v2 100 OpenGL version: 4.1 INTEL-10.36.19 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc. }}} -- Ticket URL: <https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F2932&data=02%7C01%7Ccharles.sindelar%40yale.edu%7C3a3ac28f79e242e4ea6a08d7c1ed6d67%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637191097800175941&sdata=hyxfOBWTrNlpsUa7DJFvtpHLzWACqCmsl4UWAQY8zZs%3D&reserved=0> ChimeraX <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=02%7C01%7Ccharles.sindelar%40yale.edu%7C3a3ac28f79e242e4ea6a08d7c1ed6d67%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637191097800175941&sdata=iAuCNJTeRJmax0Mf6ek8Y8f%2BgHscQMHi%2BNIuY3%2BCHd0%3D&reserved=0> ChimeraX Issue Tracker